[English] 日本語
Yorodumi
- EMDB-1017: The DnaB.DnaC complex: a structure based on dimers assembled arou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1017
TitleThe DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel.
Map data
Sample
  • Sample: DnaB.DnaC complex from Escherichia coli
  • Protein or peptide: DnaB
  • Protein or peptide: DnaC
Function / homology: / DNA helicase activity
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 26.0 Å
AuthorsBarcena M / Ruiz T / Donate LE / Brown SE / Dixon NE / Radermacher M / Carazo JM
CitationJournal: EMBO J / Year: 2001
Title: The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel.
Authors: M Bárcena / T Ruiz / L E Donate / S E Brown / N E Dixon / M Radermacher / J M Carazo /
Abstract: Replicative helicases are motor proteins that unwind DNA at replication forks. Escherichia coli DnaB is the best characterized member of this family of enzymes. We present the 26 A resolution three- ...Replicative helicases are motor proteins that unwind DNA at replication forks. Escherichia coli DnaB is the best characterized member of this family of enzymes. We present the 26 A resolution three-dimensional structure of the DnaB hexamer in complex with its loading partner, DnaC, obtained from cryo-electron microscopy. Analysis of the volume brings insight into the elaborate way the two proteins interact, and provides a structural basis for control of the symmetry state and inactivation of the helicase by DnaC. The complex is arranged on the basis of interactions among DnaC and DnaB dimers. DnaC monomers are observed for the first time to arrange as three dumb-bell-shaped dimers that interlock into one of the faces of the helicase. This could be responsible for the freezing of DnaB in a C(3) architecture by its loading partner. The central channel of the helicase is almost occluded near the end opposite to DnaC, such that even single-stranded DNA could not pass through. We propose that the DnaB N-terminal domain is located at this face.
History
DepositionJun 26, 2002-
Header (metadata) releaseOct 17, 2002-
Map releaseOct 17, 2003-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1017.gif

Downloads & links

-
Map

FileDownload / File: emd_1017.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.6 Å/pix.
x 128 pix.
= 460.8 Å		3.6 Å/pix.
x 128 pix.
= 460.8 Å		3.6 Å/pix.
x 128 pix.
= 460.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.6 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.00411 / Movie #1: 0.012
Minimum - Maximum-0.0212883 - 0.0298335
Average (Standard dev.)0.0000559347 (±0.0016241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 460.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.63.63.6
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z460.800460.800460.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0210.0300.000

-
Supplemental data

-
Sample components

-
Entire : DnaB.DnaC complex from Escherichia coli

EntireName: DnaB.DnaC complex from Escherichia coli
Components
  • Sample: DnaB.DnaC complex from Escherichia coli
  • Protein or peptide: DnaB
  • Protein or peptide: DnaC

-
Supramolecule #1000: DnaB.DnaC complex from Escherichia coli

SupramoleculeName: DnaB.DnaC complex from Escherichia coli / type: sample / ID: 1000
Oligomeric state: one homohexamer of DnaB binds to six monomers of DnaC
Number unique components: 2
Molecular weightTheoretical: 480 KDa

-
Macromolecule #1: DnaB

MacromoleculeName: DnaB / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Location in cell: cytoplasma
Molecular weightTheoretical: 310 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: An1459/pPA569
SequenceGO: DNA helicase activity / InterPro: INTERPRO: IPR001198

-
Macromolecule #2: DnaC

MacromoleculeName: DnaC / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Oligomeric state: three dimers / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Location in cell: cytoplasma
Molecular weightTheoretical: 170 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: An1459/pPA569

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.6
Details: 50 mM Tris-HCl, 25 mM NaCl 5 mM MgCl2 2 mM DTT 0.1 mM ATP
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: double-blotting

-
Electron microscopy

MicroscopeFEI/PHILIPS CM120T
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 58 / Bits/pixel: 8
Tilt angle min0
Electron beamAcceleration voltage: 100 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 57874 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000
Sample stageSpecimen holder: cryo-holder / Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 35

-
Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: OTHER / Software - Name: SPIDER and Xmipp / Number images used: 7888

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more